ISDA: 4V9Q

Deposition Date 2013-06-12

Release Date 2014-07-09

Last Version Date 2024-10-30

Entry Detail

PDB ID:

4V9Q

Keywords:

RIBOSOME

Title:

Crystal Structure of Blasticidin S Bound to Thermus Thermophilus 70S Ribosome.

Biological Source:

Source Organism:

Synthetic DNA (Taxon ID: 32630)
Thermus thermophilus (Taxon ID: 262724)
Escherichia coli (Taxon ID: 512)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.40 Å

R-Value Free:

0.26

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:Z (auth: A1), BC (auth: C1)
Chain Length:30
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72JR0 Pfam ID:PF01197

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:AA (auth: A2), CC (auth: C2)
Chain Length:52
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62652 Pfam ID:PF01783

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:BA (auth: A3), DC (auth: C3)
Chain Length:44
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72GW3 Pfam ID:PF00471

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:CA (auth: A4), EC (auth: C4)
Chain Length:48
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80340 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:DA (auth: A5), FC (auth: C5)
Chain Length:63
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72L77 Pfam ID:PF01632

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:A (auth: AA), CB (auth: CA)
Chain Length:2879
Number of Molecules:2
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: AB), DB (auth: CB)
Chain Length:119
Number of Molecules:2
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C (auth: AD), EB (auth: CD)
Chain Length:271
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I07 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D (auth: AE), FB (auth: CE)
Chain Length:204
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I04 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E (auth: AF), GB (auth: CF)
Chain Length:202
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I05 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:F (auth: AG), HB (auth: CG)
Chain Length:181
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I16 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:G (auth: AH), IB (auth: CH)
Chain Length:159
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I19 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:H (auth: AI), JB (auth: CI)
Chain Length:145
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72GV5 Pfam ID:PF03948, PF01281

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:I (auth: AJ), KB (auth: CJ)
Chain Length:137
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72IN1 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:J (auth: AK), LB (auth: CK)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I14 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:K (auth: AL), MB (auth: CL)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I23 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:L (auth: AM), NB (auth: CM)
Chain Length:134
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I11 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:M (auth: AN), OB (auth: CN)
Chain Length:117
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I33 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:N (auth: AO), PB (auth: CO)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I20 Pfam ID:PF00861

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:O (auth: AP), QB (auth: CP)
Chain Length:137
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72JU9 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:P (auth: AQ), RB (auth: CQ)
Chain Length:117
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72L76 Pfam ID:PF00453

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:Q (auth: AR), SB (auth: CR)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72HR2 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:R (auth: AS), TB (auth: CS)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I09 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:S (auth: AT), UB (auth: CT)
Chain Length:92
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I06 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:T (auth: AU), VB (auth: CU)
Chain Length:100
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I15 Pfam ID:PF00467, PF17136

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:U (auth: AV), WB (auth: CV)
Chain Length:187
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72IA7 Pfam ID:PF14693, PF01386

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:V (auth: AW), XB (auth: CW)
Chain Length:76
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72HR3 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:W (auth: AX), YB (auth: CX)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72G84 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:X (auth: AY), ZB (auth: CY)
Chain Length:62
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I12 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:Y (auth: AZ), AC (auth: CZ)
Chain Length:59
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I22 Pfam ID:PF00327

Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:EA (auth: BA), GC (auth: DA)
Chain Length:1504
Number of Molecules:2
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:FA (auth: BB), HC (auth: DB)
Chain Length:234
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62662 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:GA (auth: BC), IC (auth: DC)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62663 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:HA (auth: BD), JC (auth: DD)
Chain Length:208
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62664 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:IA (auth: BE), KC (auth: DE)
Chain Length:151
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62665 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:JA (auth: BF), LC (auth: DF)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62666 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:KA (auth: BG), MC (auth: DG)
Chain Length:155
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62667 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:LA (auth: BH), NC (auth: DH)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62668 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:MA (auth: BI), OC (auth: DI)
Chain Length:127
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62669 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:NA (auth: BJ), PC (auth: DJ)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62653 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:OA (auth: BK), QC (auth: DK)
Chain Length:114
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62654 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:PA (auth: BL), RC (auth: DL)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P61941 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:QA (auth: BM), SC (auth: DM)
Chain Length:117
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62655 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsZ
Chain IDs:RA (auth: BN), TC (auth: DN)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62656 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:SA (auth: BO), UC (auth: DO)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62657 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:TA (auth: BP), VC (auth: DP)
Chain Length:83
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62238 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:UA (auth: BQ), WC (auth: DQ)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62658 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:VA (auth: BR), XC (auth: DR)
Chain Length:70
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62659 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:WA (auth: BS), YC (auth: DS)
Chain Length:78
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62660 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:XA (auth: BT), ZC (auth: DT)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62661 Pfam ID:PF01649

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:YA (auth: BU), AD (auth: DU)
Chain Length:24
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62613 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:ZA (auth: BV), AB (auth: BW), BD (auth: DV), CD (auth: DW)
Chain Length:77
Number of Molecules:4
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:BB (auth: BX), DD (auth: DX)
Chain Length:5
Number of Molecules:2
Biological Source:Synthetic DNA

Ligand Molecules

BLS

Primary Citation

Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome.

Svidritskiy, E, Ling, C, Ermolenko, D.N, Korostelev, A.A.Show

Proc.Natl.Acad.Sci.USA 110 12283 12288 (2013)

PMID: 23824292 DOI: 10.1073/pnas.1304922110

Abstact

The antibiotic blasticidin S (BlaS) is a potent inhibitor of protein synthesis in bacteria and eukaryotes. We have determined a 3.4-Å crystal structure of BlaS bound to a 70S⋅tRNA ribosome complex and performed biochemical and single-molecule FRET experiments to determine the mechanism of action of the antibiotic. We find that BlaS enhances tRNA binding to the P site of the large ribosomal subunit and slows down spontaneous intersubunit rotation in pretranslocation ribosomes. However, the antibiotic has negligible effect on elongation factor G catalyzed translocation of tRNA and mRNA. The crystal structure of the antibiotic-ribosome complex reveals that BlaS impedes protein synthesis through a unique mechanism by bending the 3' terminus of the P-site tRNA toward the A site of the large ribosomal subunit. Biochemical experiments demonstrate that stabilization of the deformed conformation of the P-site tRNA by BlaS strongly inhibits peptidyl-tRNA hydrolysis by release factors and, to a lesser extent, peptide bond formation.

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Protein

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Disease

Primary Citation of related structures